IB DP Biology: Organelles, compartmentalization and cell specialization (DP Biology)

This guide covers sections B2.2 (Organelles and compartmentalization) and B2.3 (Cell specialization) of the IB Diploma Programme Biology guide, first assessment 2025. B2.2.1 to B2.2.3 and B2.3.1 to B2.3.6 are SL and HL. B2.2.4 to B2.2.9 and B2.3.7 to B2.3.10 are additional higher level, marked HL only. Condensed recall is in the revision notes and exam-style questions are in the practice set. See also the IB Biology hub and the printable checklist. Find weak spots with the free diagnostics.

What this unit covers

Section	You must be able to	Level
B2.2.1	Define organelles and say which cell parts count	SL and HL
B2.2.2	Explain nucleus and cytoplasm separation	SL and HL
B2.2.3	Give advantages of compartments	SL and HL
B2.2.4 to B2.2.5	Link mitochondrion and chloroplast structure to function	HL only
B2.2.6 to B2.2.9	Nuclear envelope, ribosomes, rough ER, Golgi apparatus, vesicles	HL only
B2.3.1 to B2.3.4	Differentiation, stem cells, niches, potency	SL and HL
B2.3.5 to B2.3.6	Cell size and surface area-to-volume ratio	SL and HL
B2.3.7 to B2.3.10	Specialized cells: erythrocytes, kidney tubule cells, pneumocytes, muscle, gametes	HL only

B2.2.1 Organelles

An organelle is a discrete subunit of a cell with its own structure and a specific job. The nucleus, mitochondria, chloroplasts, ribosomes, vesicles and the plasma membrane all count. The cell wall, the cytoskeleton and the cytoplasm do not count as organelles.

Organelles were hard to study until techniques arrived. In cell fractionation, you break cells open in cold, buffered, isotonic solution, then spin the homogenate in an ultracentrifuge. Denser parts pellet at lower speeds; lighter parts need higher speeds. Nuclei pellet first, then mitochondria and chloroplasts, then smaller fragments. You can then test each fraction for its own enzymes. Progress in science often follows a new technique like this.

B2.2.2 Nucleus and cytoplasm as separate compartments

In eukaryotes, transcription happens in the nucleus and translation happens on ribosomes in the cytoplasm. The separation lets the cell modify the primary transcript before any ribosome meets it. Modifications include removing introns, adding a 5’ cap and adding a poly-A tail. Only finished mRNA leaves through nuclear pores.

In prokaryotes there is no nucleus. Ribosomes can bind to an mRNA while it is still being made, so no post-transcriptional modification can come first.

B2.2.3 Compartments in the cytoplasm

Membranes divide the cytoplasm. The advantages are:

• Enzymes and substrates are concentrated in a small volume, so reactions are faster.
• Each compartment can hold its own pH.
• Incompatible processes are kept apart, so one pathway does not damage another.

Lysosomes are the clearest example. They contain hydrolytic enzymes that work best at an acidic pH, lower than the pH of the cytoplasm. If these enzymes were free in the cytoplasm they would digest proteins and other cell structures, and they would work badly at the wrong pH. A phagocytic vacuole forms when a cell engulfs a particle such as a bacterium. A lysosome fuses with it and releases enzymes into the vacuole, so digestion happens inside a membrane. Products pass into the cytoplasm.

B2.2.4 Mitochondrion (HL only)

Aerobic cell respiration makes ATP in the mitochondrion. Its adaptations:

• Double membrane with a small intermembrane space. The inner membrane pumps protons into this narrow space. A small volume means the proton concentration rises quickly, which builds the gradient that drives ATP synthase.
• Large surface area of cristae. Folds of the inner membrane carry many electron transport chains and ATP synthase molecules.
• Matrix compartment. The matrix holds the enzymes and substrates of the Krebs cycle at high concentration, away from the rest of the cytoplasm.

B2.2.5 Chloroplast (HL only)

• Large surface area of thylakoid membranes carries many photosystems and the other light-dependent components, so more light is absorbed.
• Small volume inside each thylakoid. Protons pumped in build up a gradient quickly, which drives ATP synthesis.
• Stroma compartment. The enzymes and substrates of the Calvin cycle are concentrated in the stroma.

B2.2.6 Nuclear envelope and its double membrane (HL only)

The nuclear envelope has two membranes. The pores through it let mRNA, ribosomal subunits and other molecules move out, and let proteins such as histones and enzymes for DNA replication and transcription move in. In mitosis and meiosis the envelope breaks into small vesicles. This clears the way for spindle microtubules to reach the chromosomes. The vesicles later fuse to rebuild the envelope around each new nucleus.

B2.2.7 Ribosomes and rough ER (HL only)

Eukaryotic ribosomes are 80S, made of rRNA and protein, with no membrane.

	Free ribosomes	Ribosomes on rough ER
Site	In the cytoplasm	Attached to the outer surface of the ER
Proteins made	For use inside the cell, such as glycolytic enzymes	For secretion, for lysosomes or for the plasma membrane
Fate of protein	Released into the cytosol	Enters the ER lumen, where it folds

The rough endoplasmic reticulum (rER) is a network of flattened membrane sacs, called cisternae, continuous with the outer nuclear membrane. Proteins that enter the lumen are folded and often modified, then leave in transport vesicles.

B2.2.8 Golgi apparatus (HL only)

The Golgi apparatus is a stack of flattened cisternae. Transport vesicles from the rER fuse with the receiving face. Inside, proteins are processed, for example by adding carbohydrate groups, and then sorted. Vesicles bud from the opposite face and carry proteins to the plasma membrane for secretion by exocytosis.

B2.2.9 Vesicles (HL only)

Vesicles are small membrane-bound sacs that move materials between compartments, or between a cell and its surroundings. Clathrin is a protein that assembles into a lattice-like cage on the cytoplasmic side of a membrane. The cage helps the membrane curve and pinch off as a coated vesicle, for example during endocytosis and from the Golgi apparatus.

Worked example: tracking a protein. Cells were given a brief pulse of radioactive amino acids, then moved to normal medium. Radioactivity was measured in structures over time:

Time after pulse / min	rER	Golgi	Vesicles near cell surface	Outside the cell
5	80%	10%	5%	5%
25	30%	45%	20%	5%
60	5%	15%	40%	40%

The peak moves from rER (5 min) to Golgi (25 min) to vesicles and then outside. This fits the route rER, Golgi, secretory vesicle, exocytosis, so the protein is secreted.

B2.3.1 Differentiation

After fertilization the zygote divides to give unspecialized cells. These then differentiate: each develops into a specialized cell type. All cells carry the same genome. They differ because they express different genes, so different proteins are made.

Gradients help decide which genes are expressed. In an early embryo, substances such as maternal mRNA or proteins are unevenly spread, so cells in different positions receive different concentrations. A cell reads its concentration and switches particular genes on or off.

B2.3.2 Properties of stem cells

Stem cells have two properties: they can divide endlessly (self-renewal) and they can differentiate along different pathways.

B2.3.3 Stem cell niches

A stem cell niche is the microenvironment around stem cells in an adult tissue. Its signals keep cells as stem cells or promote their division and differentiation. Two examples:

• Bone marrow. Haematopoietic stem cells give rise to blood cells, including erythrocytes and white blood cells.
• Hair follicles. Stem cells in the follicle regenerate the follicle and produce new cells for hair growth.

B2.3.4 Totipotent, pluripotent and multipotent

Type	Can become	Where found
Totipotent	Any cell type of the organism, including extra-embryonic tissue, so a whole new organism	Cells of the very early embryo
Pluripotent	Most cell types of the body, but not a whole organism	Early embryo, soon after the totipotent stage
Multipotent	A limited range of related cell types	Adult tissue, such as bone marrow

B2.3.5 and B2.3.6 Cell size and surface area-to-volume ratio

Cell size matches function. In humans an egg is about 0.1 mm across, erythrocytes about 7 µm, white blood cells somewhat larger, neurons can have axons over a metre long, and striated muscle fibres can reach several centimetres.

Exchange of materials across the surface depends on surface area. The need for exchange depends on volume. For a cube of side s:

• surface area = 6s²
• volume = s³
• surface area : volume = 6/s

Doubling the side makes the area four times larger and the volume eight times larger, so the ratio halves. A large cell cannot supply its cytoplasm fast enough. Cubes are a simplified model, but scale factors work the same way in real cells.

Worked example. Cube-shaped cells with sides 5 µm, 20 µm and 80 µm:

Side / µm	Surface area / µm²	Volume / µm³	Ratio / µm⁻¹
5	150	125	1.2
20	2400	8000	0.3
80	38 400	512 000	0.075

The ratio falls as the cell grows: it is 16 times smaller at 80 µm than at 5 µm.

Worked example: magnification. An electron micrograph is printed at ×12 000. A mitochondrion measures 54 mm long on the page. Actual length = image length ÷ magnification = 54 mm ÷ 12 000 = 0.0045 mm = 4.5 µm.

B2.3.7 Raising the ratio (HL only)

Cells raise surface area without raising volume by flattening, by microvilli and by invagination (infolding).

• Erythrocytes are biconcave discs, a flattened shape. With supplied figures, volume 90 µm³ and area 135 µm² give 1.5 µm⁻¹. A sphere of the same volume has radius 2.78 µm, an area of 97 µm² and a ratio of 1.08 µm⁻¹. The disc has about 39% more surface for the same volume, so oxygen exchange is faster.
• Proximal convoluted tubule cells have microvilli on the lumen side and infolded membranes at their base. They reabsorb a lot from the filtrate.

Worked example. A flat membrane patch is 10 µm × 10 µm (100 µm²). Add 400 microvilli, each a cylinder 0.1 µm wide and 1 µm tall. Each adds a side area of π × 0.1 × 1 = 0.314 µm², which is 125.7 µm² in total. The tip of each cylinder replaces the flat area it covers. New area = 225.7 µm², about 2.3 times the original.

B2.3.8 Pneumocytes (HL only)

The alveolar epithelium holds two cell types, because the tissue needs two kinds of adaptation.

• Type I pneumocytes are extremely thin and flat, which shortens the diffusion distance between air and blood.
• Type II pneumocytes have many vesicles called lamellar bodies in the cytoplasm. They discharge surfactant into the alveolar lumen, which reduces surface tension and keeps the alveoli from sticking shut.

B2.3.9 Muscle cells (HL only)

Both muscle types contain contractile myofibrils. They differ in structure:

• Cardiac muscle cells are branched, and usually have one or two nuclei. Branching may help contraction spread in several directions.
• Striated muscle fibres are unbranched, very long and have many nuclei. Many nuclei may support the large cytoplasm.

These are hypotheses for the differences. A striated muscle fibre is a debated case for the cell definition: it is far larger than a typical cell and multinucleate, formed by many cells fusing, but it is enclosed by a single plasma membrane. Be ready to argue both ways.

B2.3.10 Gametes (HL only)

• Sperm cell: small, with a flagellum for swimming, many mitochondria in the midpiece for ATP, and an acrosome containing digestive enzymes that help penetrate the egg’s outer layers.
• Egg cell: large and non-motile, with a big cytoplasm containing food reserves, and an outer layer that changes after one sperm enters to prevent entry of more.

Worked example. An egg is modelled as a sphere of radius 60 µm. Surface area to volume = 3/r = 3/60 = 0.05 µm⁻¹, well below the cube cells above.

Common errors

• Calling the cell wall or cytoplasm an organelle.
• Saying a larger cell has a larger SA:V ratio. Area grows more slowly than volume.
• Mixing up free ribosomes (proteins kept in the cell) and rER ribosomes (secreted proteins).

Official syllabus

International Baccalaureate Organization, Diploma Programme Biology guide, first assessment 2025, published February 2023, sections B2.2 and B2.3.